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Kim GD, Qiu D, Jessen HJ, Mayer A. Metabolic Consequences of Polyphosphate Synthesis and Imminent Phosphate Limitation. mBio 2023; 14:e0010223. [PMID: 37074217 PMCID: PMC10294617 DOI: 10.1128/mbio.00102-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 03/22/2023] [Indexed: 04/20/2023] Open
Abstract
Cells stabilize intracellular inorganic phosphate (Pi) to compromise between large biosynthetic needs and detrimental bioenergetic effects of Pi. Pi homeostasis in eukaryotes uses Syg1/Pho81/Xpr1 (SPX) domains, which are receptors for inositol pyrophosphates. We explored how polymerization and storage of Pi in acidocalcisome-like vacuoles supports Saccharomyces cerevisiae metabolism and how these cells recognize Pi scarcity. Whereas Pi starvation affects numerous metabolic pathways, beginning Pi scarcity affects few metabolites. These include inositol pyrophosphates and ATP, a low-affinity substrate for inositol pyrophosphate-synthesizing kinases. Declining ATP and inositol pyrophosphates may thus be indicators of impending Pi limitation. Actual Pi starvation triggers accumulation of the purine synthesis intermediate 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR), which activates Pi-dependent transcription factors. Cells lacking inorganic polyphosphate show Pi starvation features already under Pi-replete conditions, suggesting that vacuolar polyphosphate supplies Pi for metabolism even when Pi is abundant. However, polyphosphate deficiency also generates unique metabolic changes that are not observed in starving wild-type cells. Polyphosphate in acidocalcisome-like vacuoles may hence be more than a global phosphate reserve and channel Pi to preferred cellular processes. IMPORTANCE Cells must strike a delicate balance between the high demand of inorganic phosphate (Pi) for synthesizing nucleic acids and phospholipids and its detrimental bioenergetic effects by reducing the free energy of nucleotide hydrolysis. The latter may stall metabolism. Therefore, microorganisms manage the import and export of phosphate, its conversion into osmotically inactive inorganic polyphosphates, and their storage in dedicated organelles (acidocalcisomes). Here, we provide novel insights into metabolic changes that yeast cells may use to signal declining phosphate availability in the cytosol and differentiate it from actual phosphate starvation. We also analyze the role of acidocalcisome-like organelles in phosphate homeostasis. This study uncovers an unexpected role of the polyphosphate pool in these organelles under phosphate-rich conditions, indicating that its metabolic roles go beyond that of a phosphate reserve for surviving starvation.
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Affiliation(s)
- Geun-Don Kim
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
| | | | - Andreas Mayer
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
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2
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Uvdal P, Shashkova S. The Effect of Calorie Restriction on Protein Quality Control in Yeast. Biomolecules 2023; 13:biom13050841. [PMID: 37238710 DOI: 10.3390/biom13050841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/30/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023] Open
Abstract
Initially, protein aggregates were regarded as a sign of a pathological state of the cell. Later, it was found that these assemblies are formed in response to stress, and that some of them serve as signalling mechanisms. This review has a particular focus on how intracellular protein aggregates are related to altered metabolism caused by different glucose concentrations in the extracellular environment. We summarise the current knowledge of the role of energy homeostasis signalling pathways in the consequent effect on intracellular protein aggregate accumulation and removal. This covers regulation at different levels, including elevated protein degradation and proteasome activity mediated by the Hxk2 protein, the enhanced ubiquitination of aberrant proteins through Torc1/Sch9 and Msn2/Whi2, and the activation of autophagy mediated through ATG genes. Finally, certain proteins form reversible biomolecular aggregates in response to stress and reduced glucose levels, which are used as a signalling mechanism in the cell, controlling major primary energy pathways related to glucose sensing.
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Affiliation(s)
- Petter Uvdal
- Department of Physics, University of Gothenburg, 405 30 Göteborg, Sweden
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3
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Groth B, Lee YC, Huang CC, McDaniel M, Huang K, Lee LH, Lin SJ. The Histone Deacetylases Hst1 and Rpd3 Integrate De Novo NAD + Metabolism with Phosphate Sensing in Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:ijms24098047. [PMID: 37175754 PMCID: PMC10179157 DOI: 10.3390/ijms24098047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/22/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) is a critical cofactor essential for various cellular processes. Abnormalities in NAD+ metabolism have also been associated with a number of metabolic disorders. The regulation and interconnection of NAD+ metabolic pathways are not yet completely understood. By employing an NAD+ intermediate-specific genetic system established in the model organism S. cerevisiae, we show that histone deacetylases (HDACs) Hst1 and Rpd3 link the regulation of the de novo NAD+ metabolism-mediating BNA genes with certain aspects of the phosphate (Pi)-sensing PHO pathway. Our genetic and gene expression studies suggest that the Bas1-Pho2 and Pho2-Pho4 transcription activator complexes play a role in this co-regulation. Our results suggest a model in which competition for Pho2 usage between the BNA-activating Bas1-Pho2 complex and the PHO-activating Pho2-Pho4 complex helps balance de novo activity with PHO activity in response to NAD+ or phosphate depletion. Interestingly, both the Bas1-Pho2 and Pho2-Pho4 complexes appear to also regulate the expression of the salvage-mediating PNC1 gene negatively. These results suggest a mechanism for the inverse regulation between the NAD+ salvage pathways and the de novo pathway observed in our genetic models. Our findings help provide a molecular basis for the complex interplay of two different aspects of cellular metabolism.
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Affiliation(s)
- Benjamin Groth
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Yi-Ching Lee
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Chi-Chun Huang
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Matilda McDaniel
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Katie Huang
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Lan-Hsuan Lee
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Su-Ju Lin
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
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4
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Takaine M, Imamura H, Yoshida S. High and stable ATP levels prevent aberrant intracellular protein aggregation in yeast. eLife 2022; 11:67659. [PMID: 35438635 PMCID: PMC9018071 DOI: 10.7554/elife.67659] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/18/2022] [Indexed: 12/24/2022] Open
Abstract
Adenosine triphosphate (ATP) at millimolar levels has recently been implicated in the solubilization of cellular proteins. However, the significance of this high ATP level under physiological conditions and the mechanisms that maintain ATP remain unclear. We herein demonstrated that AMP-activated protein kinase (AMPK) and adenylate kinase (ADK) cooperated to maintain cellular ATP levels regardless of glucose levels. Single-cell imaging of ATP-reduced yeast mutants revealed that ATP levels in these mutants underwent stochastic and transient depletion, which promoted the cytotoxic aggregation of endogenous proteins and pathogenic proteins, such as huntingtin and α-synuclein. Moreover, pharmacological elevations in ATP levels in an ATP-reduced mutant prevented the accumulation of α-synuclein aggregates and its cytotoxicity. The present study demonstrates that cellular ATP homeostasis ensures proteostasis and revealed that suppressing the high volatility of cellular ATP levels prevented cytotoxic protein aggregation, implying that AMPK and ADK are important factors that prevent proteinopathies, such as neurodegenerative diseases. Cells use a chemical called adenosine triphosphate (ATP) as a controllable source of energy. Like a battery, each ATP molecule contains a specific amount of energy that can be released when needed. Cells just need enough ATP to survive, but most cells store a lot more than they need. It is unclear why cells keep so much ATP, or whether this excess ATP has any other purpose. To answer these questions, Takaine et al. identified mutants of the yeast Saccharomyces cerevisiae that had low levels of ATP, and studied how these cells differ from normal yeast The results showed that, in S. cerevisiae cells with lower and variable levels of ATP, proteins stick together, forming clumps. Proteins are molecules that perform diverse roles, keeping cells alive. When they clump together, they stop working and can cause cells to die. Further experiments showed that reducing the levels of ATP just for a short time increased the rate at which proteins stick together. Taken together, Takaine et al.’s results suggest that ATP plays a role in stopping proteins from sticking together, explaining why cells may store excess ATP, since it could aid survival. Protein clumps, also called aggregates, are a key feature of various illnesses, including neurodegenerative diseases such as Alzheimer’s. Takaine et al. provide a possible cause for why proteins aggregate in these diseases, which may be worth further study.
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Affiliation(s)
- Masak Takaine
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Japan.,Institute for Molecular and Cellular Regulation (IMCR), Gunma University, Maebashi, Japan
| | - Hiromi Imamura
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Satoshi Yoshida
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Japan.,Institute for Molecular and Cellular Regulation (IMCR), Gunma University, Maebashi, Japan.,School of International Liberal Studies, Waseda University, Tokyo, Japan.,Japan Science and Technology Agency, PREST, Tokyo, Japan
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5
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Tan S, Chen Y, Zhou G, Liu J. Transcriptome Analysis of Colletotrichum fructicola Infecting Camellia oleifera Indicates That Two Distinct Geographical Fungi Groups Have Different Destructive Proliferation Capacities Related to Purine Metabolism. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122672. [PMID: 34961144 PMCID: PMC8708221 DOI: 10.3390/plants10122672] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 05/02/2023]
Abstract
Anthracnose, caused by Colletotrichum spp., is a significant disease affecting oil tea (Camellia oleifera Abel.). Extensive molecular studies have demonstrated that Colletotrichum fructicola is the dominant pathogen of oil tea anthracnose in China. This study aims to investigate differences in molecular processes and regulatory genes at a late stage of infection of C. fructicola, to aid in understanding differences in pathogenic mechanisms of C. fructicola of different geographic populations. We compared the pathogenicity of C. fructicola from different populations (Wuzhishan, Hainan province, and Shaoyang, Hunan province) and gene expression of representative strains of the two populations before and after inoculation in oil tea using RNA sequencing. The results revealed that C. fructicola from Wuzhishan has a more vital ability to impact oil tea leaf tissue. Following infection with oil tea leaves, up-regulated genes in the strains from two geographic populations were associated with galactosidase activity, glutamine family amino acid metabolism, arginine, and proline metabolism. Additionally, up-regulated gene lists associated with infection by Wuzhishan strains were significantly enriched in purine metabolism pathways, while Shaoyang strains were not. These results indicate that more transcriptional and translational activity and the greater regulation of the purine metabolism pathway in the C. fructicola of the Wuzhishan strain might contribute to its stronger pathogenicity.
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Affiliation(s)
- Shimeng Tan
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Central South University of Forestry and Technology, Changsha 410004, China; (S.T.); (Y.C.); (G.Z.)
- Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Central South University of Forestry and Technology, Changsha 410004, China
- Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
- College of Biological Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Yanying Chen
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Central South University of Forestry and Technology, Changsha 410004, China; (S.T.); (Y.C.); (G.Z.)
- Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Central South University of Forestry and Technology, Changsha 410004, China
- Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
- College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Guoying Zhou
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Central South University of Forestry and Technology, Changsha 410004, China; (S.T.); (Y.C.); (G.Z.)
- Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Central South University of Forestry and Technology, Changsha 410004, China
- Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
- College of Biological Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Junang Liu
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Central South University of Forestry and Technology, Changsha 410004, China; (S.T.); (Y.C.); (G.Z.)
- Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Central South University of Forestry and Technology, Changsha 410004, China
- Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
- College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
- Correspondence:
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6
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Bonnet A, Chaput C, Palmic N, Palancade B, Lesage P. A nuclear pore sub-complex restricts the propagation of Ty retrotransposons by limiting their transcription. PLoS Genet 2021; 17:e1009889. [PMID: 34723966 PMCID: PMC8585004 DOI: 10.1371/journal.pgen.1009889] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 11/11/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022] Open
Abstract
Beyond their canonical function in nucleocytoplasmic exchanges, nuclear pore complexes (NPCs) regulate the expression of protein-coding genes. Here, we have implemented transcriptomic and molecular methods to specifically address the impact of the NPC on retroelements, which are present in multiple copies in genomes. We report a novel function for the Nup84 complex, a core NPC building block, in specifically restricting the transcription of LTR-retrotransposons in yeast. Nup84 complex-dependent repression impacts both Copia and Gypsy Ty LTR-retrotransposons, all over the S. cerevisiae genome. Mechanistically, the Nup84 complex restricts the transcription of Ty1, the most active yeast retrotransposon, through the tethering of the SUMO-deconjugating enzyme Ulp1 to NPCs. Strikingly, the modest accumulation of Ty1 RNAs caused by Nup84 complex loss-of-function is sufficient to trigger an important increase of Ty1 cDNA levels, resulting in massive Ty1 retrotransposition. Altogether, our study expands our understanding of the complex interactions between retrotransposons and the NPC, and highlights the importance for the cells to keep retrotransposons under tight transcriptional control.
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Affiliation(s)
- Amandine Bonnet
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Carole Chaput
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
| | - Noé Palmic
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
| | - Benoit Palancade
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Pascale Lesage
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
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7
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Luzarowski M, Vicente R, Kiselev A, Wagner M, Schlossarek D, Erban A, de Souza LP, Childs D, Wojciechowska I, Luzarowska U, Górka M, Sokołowska EM, Kosmacz M, Moreno JC, Brzezińska A, Vegesna B, Kopka J, Fernie AR, Willmitzer L, Ewald JC, Skirycz A. Global mapping of protein-metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity. Commun Biol 2021; 4:181. [PMID: 33568709 PMCID: PMC7876005 DOI: 10.1038/s42003-021-01684-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/08/2021] [Indexed: 01/30/2023] Open
Abstract
Protein-metabolite interactions are of crucial importance for all cellular processes but remain understudied. Here, we applied a biochemical approach named PROMIS, to address the complexity of the protein-small molecule interactome in the model yeast Saccharomyces cerevisiae. By doing so, we provide a unique dataset, which can be queried for interactions between 74 small molecules and 3982 proteins using a user-friendly interface available at https://promis.mpimp-golm.mpg.de/yeastpmi/ . By interpolating PROMIS with the list of predicted protein-metabolite interactions, we provided experimental validation for 225 binding events. Remarkably, of the 74 small molecules co-eluting with proteins, 36 were proteogenic dipeptides. Targeted analysis of a representative dipeptide, Ser-Leu, revealed numerous protein interactors comprising chaperones, proteasomal subunits, and metabolic enzymes. We could further demonstrate that Ser-Leu binding increases activity of a glycolytic enzyme phosphoglycerate kinase (Pgk1). Consistent with the binding analysis, Ser-Leu supplementation leads to the acute metabolic changes and delays timing of a diauxic shift. Supported by the dipeptide accumulation analysis our work attests to the role of Ser-Leu as a metabolic regulator at the interface of protein degradation and central metabolism.
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Affiliation(s)
- Marcin Luzarowski
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Rubén Vicente
- grid.418390.70000 0004 0491 976XDepartment of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Andrei Kiselev
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.503344.50000 0004 0445 6769Laboratoire de Recherche en Sciences Végétales (LRSV), UPS/CNRS, UMR, Castanet Tolosan, France
| | - Mateusz Wagner
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.8505.80000 0001 1010 5103University of Wrocław, Faculty of Biotechnology, Laboratory of Medical Biology, Wrocław, Poland
| | - Dennis Schlossarek
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Alexander Erban
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Leonardo Perez de Souza
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Dorothee Childs
- grid.4709.a0000 0004 0495 846XDepartment of Genome Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Izabela Wojciechowska
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Urszula Luzarowska
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.7489.20000 0004 1937 0511Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michał Górka
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Ewelina M. Sokołowska
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Monika Kosmacz
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.45672.320000 0001 1926 5090Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Juan C. Moreno
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.45672.320000 0001 1926 5090Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Aleksandra Brzezińska
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Bhavana Vegesna
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Joachim Kopka
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Alisdair R. Fernie
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Lothar Willmitzer
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Jennifer C. Ewald
- grid.10392.390000 0001 2190 1447Interfaculty Institute of Cell Biology, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Aleksandra Skirycz
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.5386.8000000041936877XBoyce Thompson Institute, Ithaca, NY USA
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Yague-Sanz C, Vanrobaeys Y, Fernandez R, Duval M, Larochelle M, Beaudoin J, Berro J, Labbé S, Jacques PÉ, Bachand F. Nutrient-dependent control of RNA polymerase II elongation rate regulates specific gene expression programs by alternative polyadenylation. Genes Dev 2020; 34:883-897. [PMID: 32499400 PMCID: PMC7328516 DOI: 10.1101/gad.337212.120] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/06/2020] [Indexed: 12/22/2022]
Abstract
In this study from Yague-Sanz et al., the authors investigated the physiological relevance of variations in RNAPII elongation kinetics, and show in yeast that a RNAPII mutant that reduces the transcription elongation rate causes widespread changes in alternative polyadenylation (APA). Their findings indicate that RNAPII is a sensor of nucleotide availability and that genes important for nucleotide pool maintenance have adopted regulatory mechanisms responsive to reduced rates of transcription elongation. Transcription by RNA polymerase II (RNAPII) is a dynamic process with frequent variations in the elongation rate. However, the physiological relevance of variations in RNAPII elongation kinetics has remained unclear. Here we show in yeast that a RNAPII mutant that reduces the transcription elongation rate causes widespread changes in alternative polyadenylation (APA). We unveil two mechanisms by which APA affects gene expression in the slow mutant: 3′ UTR shortening and gene derepression by premature transcription termination of upstream interfering noncoding RNAs. Strikingly, the genes affected by these mechanisms are enriched for functions involved in phosphate uptake and purine synthesis, processes essential for maintenance of the intracellular nucleotide pool. As nucleotide concentration regulates transcription elongation, our findings argue that RNAPII is a sensor of nucleotide availability and that genes important for nucleotide pool maintenance have adopted regulatory mechanisms responsive to reduced rates of transcription elongation.
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Affiliation(s)
- Carlo Yague-Sanz
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Yann Vanrobaeys
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Ronan Fernandez
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut 06520, USA.,Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Maxime Duval
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Marc Larochelle
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Jude Beaudoin
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Julien Berro
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut 06520, USA.,Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Simon Labbé
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | | | - François Bachand
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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9
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Phosphate in Virulence of Candida albicans and Candida glabrata. J Fungi (Basel) 2020; 6:jof6020040. [PMID: 32224872 PMCID: PMC7344514 DOI: 10.3390/jof6020040] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/21/2020] [Accepted: 03/22/2020] [Indexed: 12/22/2022] Open
Abstract
Candida species are the most commonly isolated invasive human fungal pathogens. A role for phosphate acquisition in their growth, resistance against host immune cells, and tolerance of important antifungal medications is becoming apparent. Phosphorus is an essential element in vital components of the cell, including chromosomes and ribosomes. Producing the energy currency of the cell, ATP, requires abundant inorganic phosphate. A comparison of the network of regulators and effectors that controls phosphate acquisition and intracellular distribution, the PHO regulon, between the model yeast Saccharomyces cerevisiae, a plant saprobe, its evolutionarily close relative C. glabrata, and the more distantly related C. albicans, highlights the need to coordinate phosphate homeostasis with adenylate biosynthesis for ATP production. It also suggests that fungi that cope with phosphate starvation as they invade host tissues, may link phosphate acquisition to stress responses as an efficient mechanism of anticipatory regulation. Recent work indicates that connections among the PHO regulon, Target of Rapamycin Complex 1 signaling, oxidative stress management, and cell wall construction are based both in direct signaling links, and in the provision of phosphate for sufficient metabolic intermediates that are substrates in these processes. Fundamental differences in fungal and human phosphate homeostasis may offer novel drug targets.
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10
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Su X, Lu G, Li X, Rehman L, Liu W, Sun G, Guo H, Wang G, Cheng H. Host-Induced Gene Silencing of an Adenylate Kinase Gene Involved in Fungal Energy Metabolism Improves Plant Resistance to Verticillium dahliae. Biomolecules 2020; 10:E127. [PMID: 31940882 PMCID: PMC7023357 DOI: 10.3390/biom10010127] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/10/2020] [Accepted: 01/10/2020] [Indexed: 12/11/2022] Open
Abstract
Verticillium wilt, caused by the ascomycete fungus Verticillium dahliae (Vd), is a devastating disease of numerous plant species. However, the pathogenicity/virulence-related genes in this fungus, which may be potential targets for improving plant resistance, remain poorly elucidated. For the study of these genes in Vd, we used a well-established host-induced gene silencing (HIGS) approach and identified 16 candidate genes, including a putative adenylate kinase gene (VdAK). Transiently VdAK-silenced plants developed milder wilt symptoms than control plants did. VdAK-knockout mutants were more sensitive to abiotic stresses and had reduced germination and virulence on host plants. Transgenic Nicotiana benthamiana and Arabidopsis thaliana plants that overexpressed VdAK dsRNAs had improved Vd resistance than the wild-type. RT-qPCR results showed that VdAK was also crucial for energy metabolism. Importantly, in an analysis of total small RNAs from Vd strains isolated from the transgenic plants, a small interfering RNA (siRNA) targeting VdAK was identified in transgenic N. benthamiana. Our results demonstrate that HIGS is a promising strategy for efficiently screening pathogenicity/virulence-related genes of Vd and that VdAK is a potential target to control this fungus.
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Affiliation(s)
- Xiaofeng Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.S.); (G.L.); (X.L.); (L.R.); (G.S.); (H.G.)
| | - Guoqing Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.S.); (G.L.); (X.L.); (L.R.); (G.S.); (H.G.)
| | - Xiaokang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.S.); (G.L.); (X.L.); (L.R.); (G.S.); (H.G.)
| | - Latifur Rehman
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.S.); (G.L.); (X.L.); (L.R.); (G.S.); (H.G.)
- Department of Biotechnology, University of Swabi, Khyber Pakhtunkhwa 23561, Pakistan
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Guoqing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.S.); (G.L.); (X.L.); (L.R.); (G.S.); (H.G.)
| | - Huiming Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.S.); (G.L.); (X.L.); (L.R.); (G.S.); (H.G.)
| | - Guoliang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA
| | - Hongmei Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.S.); (G.L.); (X.L.); (L.R.); (G.S.); (H.G.)
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11
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Paramasivan K, Kumar HN P, Mutturi S. Systems-based Saccharomyces cerevisiae strain design for improved squalene synthesis. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.04.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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Takaine M, Ueno M, Kitamura K, Imamura H, Yoshida S. Reliable imaging of ATP in living budding and fission yeast. J Cell Sci 2019; 132:jcs.230649. [PMID: 30858198 DOI: 10.1242/jcs.230649] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/04/2019] [Indexed: 01/12/2023] Open
Abstract
Adenosine triphosphate (ATP) is a main metabolite essential for all living organisms. However, our understanding of ATP dynamics within a single living cell is very limited. Here, we optimized the ATP-biosensor QUEEN and monitored the dynamics of ATP with good spatial and temporal resolution in living yeasts. We found stable maintenance of ATP concentration in wild-type yeasts, regardless of carbon sources or cell cycle stages, suggesting that mechanism exists to maintain ATP at a specific concentration. We further found that ATP concentration is not necessarily an indicator of metabolic activity, as there is no clear correlation between ATP level and growth rates. During fission yeast meiosis, we found a reduction in ATP levels, suggesting that ATP homeostasis is controlled by differentiation. The use of QUEEN in yeasts offers an easy and reliable assay for ATP dynamicity and will answer several unaddressed questions about cellular metabolism in eukaryotes.
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Affiliation(s)
- Masak Takaine
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi 371-8512, Japan .,Institute for Molecular and Cellular Regulation (IMCR), Gunma University, Maebashi 371-8512, Japan
| | - Masaru Ueno
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Japan.,Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Japan
| | - Kenji Kitamura
- Center for Gene Science, Hiroshima University, 1-4-2 Kagamiyama, Higashi-Hiroshima 739-8527, Japan
| | - Hiromi Imamura
- Department of Functional Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Satoshi Yoshida
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi 371-8512, Japan .,Institute for Molecular and Cellular Regulation (IMCR), Gunma University, Maebashi 371-8512, Japan.,School of International Liberal Studies, Waseda University, Tokyo, 169-8050, Japan.,Japan Science and Technology Agency, PREST
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13
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Pinson B, Ceschin J, Saint-Marc C, Daignan-Fornier B. Dual control of NAD + synthesis by purine metabolites in yeast. eLife 2019; 8:43808. [PMID: 30860478 PMCID: PMC6430606 DOI: 10.7554/elife.43808] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
Metabolism is a highly integrated process resulting in energy and biomass production. While individual metabolic routes are well characterized, the mechanisms ensuring crosstalk between pathways are poorly described, although they are crucial for homeostasis. Here, we establish a co-regulation of purine and pyridine metabolism in response to external adenine through two separable mechanisms. First, adenine depletion promotes transcriptional upregulation of the de novo NAD+ biosynthesis genes by a mechanism requiring the key-purine intermediates ZMP/SZMP and the Bas1/Pho2 transcription factors. Second, adenine supplementation favors the pyridine salvage route resulting in an ATP-dependent increase of intracellular NAD+. This control operates at the level of the nicotinic acid mononucleotide adenylyl-transferase Nma1 and can be bypassed by overexpressing this enzyme. Therefore, in yeast, pyridine metabolism is under the dual control of ZMP/SZMP and ATP, revealing a much wider regulatory role for these intermediate metabolites in an integrated biosynthesis network.
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Affiliation(s)
- Benoît Pinson
- IBGCUniversité de Bordeaux UMR 5095BordeauxFrance
- Centre National de la Recherche Scientifique IBGC UMR 5095BordeauxFrance
| | - Johanna Ceschin
- IBGCUniversité de Bordeaux UMR 5095BordeauxFrance
- Centre National de la Recherche Scientifique IBGC UMR 5095BordeauxFrance
| | - Christelle Saint-Marc
- IBGCUniversité de Bordeaux UMR 5095BordeauxFrance
- Centre National de la Recherche Scientifique IBGC UMR 5095BordeauxFrance
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14
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Tükenmez H, Magnussen HM, Kovermann M, Byström A, Wolf-Watz M. Linkage between Fitness of Yeast Cells and Adenylate Kinase Catalysis. PLoS One 2016; 11:e0163115. [PMID: 27642758 PMCID: PMC5028032 DOI: 10.1371/journal.pone.0163115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/03/2016] [Indexed: 01/08/2023] Open
Abstract
Enzymes have evolved with highly specific values of their catalytic parameters kcat and KM. This poses fundamental biological questions about the selection pressures responsible for evolutionary tuning of these parameters. Here we are address these questions for the enzyme adenylate kinase (Adk) in eukaryotic yeast cells. A plasmid shuffling system was developed to allow quantification of relative fitness (calculated from growth rates) of yeast in response to perturbations of Adk activity introduced through mutations. Biophysical characterization verified that all variants studied were properly folded and that the mutations did not cause any substantial differences to thermal stability. We found that cytosolic Adk is essential for yeast viability in our strain background and that viability could not be restored with a catalytically dead, although properly folded Adk variant. There exist a massive overcapacity of Adk catalytic activity and only 12% of the wild type kcat is required for optimal growth at the stress condition 20°C. In summary, the approach developed here has provided new insights into the evolutionary tuning of kcat for Adk in a eukaryotic organism. The developed methodology may also become useful for uncovering new aspects of active site dynamics and also in enzyme design since a large library of enzyme variants can be screened rapidly by identifying viable colonies.
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Affiliation(s)
- Hasan Tükenmez
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | | | | | - Anders Byström
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
- * E-mail: (MWW); (AB)
| | - Magnus Wolf-Watz
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden
- * E-mail: (MWW); (AB)
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15
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Interactions Between Monovalent Cations and Nutrient Homeostasis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:271-289. [PMID: 26721278 DOI: 10.1007/978-3-319-25304-6_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Maintenance of appropriate fluxes of monovalent cation is a requirement for growth and survival. In the budding yeast Saccharomyces cerevisiae an electrochemical gradient of H(+) is fundamental for the uptake of diverse cations, such as K(+), and of many other nutrients. In spite of early work suggesting that alterations in monovalent cation fluxes impact on the uptake and utilization of nutrients, such as phosphate anions, only recently this important aspect of the yeast physiology has been addressed and characterized in some detail. This chapter provides a historical background and summarizes the latest findings.
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16
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Ceschin J, Hürlimann HC, Saint-Marc C, Albrecht D, Violo T, Moenner M, Daignan-Fornier B, Pinson B. Disruption of Nucleotide Homeostasis by the Antiproliferative Drug 5-Aminoimidazole-4-carboxamide-1-β-d-ribofuranoside Monophosphate (AICAR). J Biol Chem 2015; 290:23947-59. [PMID: 26283791 DOI: 10.1074/jbc.m115.656017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 11/06/2022] Open
Abstract
5-Aminoimidazole-4-carboxamide-1-β-D-ribofuranoside monophosphate (AICAR) is a natural metabolite with potent anti-proliferative and low energy mimetic properties. At high concentration, AICAR is toxic for yeast and mammalian cells, but the molecular basis of this toxicity is poorly understood. Here, we report the identification of yeast purine salvage pathway mutants that are synthetically lethal with AICAR accumulation. Genetic suppression revealed that this synthetic lethality is in part due to low expression of adenine phosphoribosyl transferase under high AICAR conditions. In addition, metabolite profiling points to the AICAR/NTP balance as crucial for optimal utilization of glucose as a carbon source. Indeed, we found that AICAR toxicity in yeast and human cells is alleviated when glucose is replaced by an alternative carbon source. Together, our metabolic analyses unveil the AICAR/NTP balance as a major factor of AICAR antiproliferative effects.
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Affiliation(s)
- Johanna Ceschin
- From the Université de Bordeaux and the Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires UMR 5095, Saint-Saëns, F-33077 Bordeaux, France
| | - Hans Caspar Hürlimann
- From the Université de Bordeaux and the Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires UMR 5095, Saint-Saëns, F-33077 Bordeaux, France
| | - Christelle Saint-Marc
- From the Université de Bordeaux and the Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires UMR 5095, Saint-Saëns, F-33077 Bordeaux, France
| | - Delphine Albrecht
- From the Université de Bordeaux and the Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires UMR 5095, Saint-Saëns, F-33077 Bordeaux, France
| | - Typhaine Violo
- From the Université de Bordeaux and the Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires UMR 5095, Saint-Saëns, F-33077 Bordeaux, France
| | - Michel Moenner
- From the Université de Bordeaux and the Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires UMR 5095, Saint-Saëns, F-33077 Bordeaux, France
| | - Bertrand Daignan-Fornier
- From the Université de Bordeaux and the Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires UMR 5095, Saint-Saëns, F-33077 Bordeaux, France
| | - Benoît Pinson
- From the Université de Bordeaux and the Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires UMR 5095, Saint-Saëns, F-33077 Bordeaux, France
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17
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Tsang F, Lin SJ. Less is more: Nutrient limitation induces cross-talk of nutrient sensing pathways with NAD + homeostasis and contributes to longevity. ACTA ACUST UNITED AC 2015; 10:333-357. [PMID: 27683589 DOI: 10.1007/s11515-015-1367-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nutrient sensing pathways and their regulation grant cells control over their metabolism and growth in response to changing nutrients. Factors that regulate nutrient sensing can also modulate longevity. Reduced activity of nutrient sensing pathways such as glucose-sensing PKA, nitrogen-sensing TOR and S6 kinase homolog Sch9 have been linked to increased life span in the yeast, Saccharomyces cerevisiae, and higher eukaryotes. Recently, reduced activity of amino acid sensing SPS pathway was also shown to increase yeast life span. Life span extension by reduced SPS activity requires enhanced NAD+ (nicotinamide adenine dinucleotide, oxidized form) and nicotinamide riboside (NR, a NAD+ precursor) homeostasis. Maintaining adequate NAD+ pools has been shown to play key roles in life span extension, but factors regulating NAD+ metabolism and homeostasis are not completely understood. Recently, NAD+ metabolism was also linked to the phosphate (Pi)-sensing PHO pathway in yeast. Canonical PHO activation requires Pi-starvation. Interestingly, NAD+ depletion without Pi-starvation was sufficient to induce PHO activation, increasing NR production and mobilization. Moreover, SPS signaling appears to function in parallel with PHO signaling components to regulate NR/NAD+ homeostasis. These studies suggest that NAD+ metabolism is likely controlled by and/or coordinated with multiple nutrient sensing pathways. Indeed, cross-regulation of PHO, PKA, TOR and Sch9 pathways was reported to potentially affect NAD+ metabolism; though detailed mechanisms remain unclear. This review discusses yeast longevity-related nutrient sensing pathways and possible mechanisms of life span extension, regulation of NAD+ homeostasis, and cross-talk among nutrient sensing pathways and NAD+ homeostasis.
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Affiliation(s)
- Felicia Tsang
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Su-Ju Lin
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
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18
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Dissection of the PHO pathway in Schizosaccharomyces pombe using epistasis and the alternate repressor adenine. Curr Genet 2014; 61:175-83. [DOI: 10.1007/s00294-014-0466-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 12/11/2014] [Accepted: 12/15/2014] [Indexed: 12/27/2022]
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19
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Canadell D, González A, Casado C, Ariño J. Functional interactions between potassium and phosphate homeostasis in Saccharomyces cerevisiae. Mol Microbiol 2014; 95:555-72. [PMID: 25425491 DOI: 10.1111/mmi.12886] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2014] [Indexed: 12/29/2022]
Abstract
Maintenance of ion homeostatic mechanisms is essential for living cells, including the budding yeast Saccharomyces cerevisiae. Whereas the impact of changes in phosphate metabolism on metal ion homeostasis has been recently examined, the inverse effect is still largely unexplored. We show here that depletion of potassium from the medium or alteration of diverse regulatory pathways controlling potassium uptake, such as the Trk potassium transporters or the Pma1 H(+) -ATPase, triggers a response that mimics that of phosphate (Pi) deprivation, exemplified by accumulation of the high-affinity Pi transporter Pho84. This response is mediated by and requires the integrity of the PHO signaling pathway. Removal of potassium from the medium does not alter the amount of total or free intracellular Pi, but is accompanied by decreased ATP and ADP levels and rapid depletion of cellular polyphosphates. Therefore, our data do not support the notion of Pi being the major signaling molecule triggering phosphate-starvation responses. We also observe that cells with compromised potassium uptake cannot grow under limiting Pi conditions. The link between potassium and phosphate homeostasis reported here could explain the invasive phenotype, characteristic of nutrient deprivation, observed in potassium-deficient yeast cells.
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Affiliation(s)
- David Canadell
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
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20
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21
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Verma M, Zakhartsev M, Reuss M, Westerhoff HV. 'Domino' systems biology and the 'A' of ATP. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:19-29. [PMID: 23031542 DOI: 10.1016/j.bbabio.2012.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 09/17/2012] [Accepted: 09/23/2012] [Indexed: 11/30/2022]
Abstract
We develop a strategic 'domino' approach that starts with one key feature of cell function and the main process providing for it, and then adds additional processes and components only as necessary to explain provoked experimental observations. The approach is here applied to the energy metabolism of yeast in a glucose limited chemostat, subjected to a sudden increase in glucose. The puzzles addressed include (i) the lack of increase in adenosine triphosphate (ATP) upon glucose addition, (ii) the lack of increase in adenosine diphosphate (ADP) when ATP is hydrolyzed, and (iii) the rapid disappearance of the 'A' (adenine) moiety of ATP. Neither the incorporation of nucleotides into new biomass, nor steady de novo synthesis of adenosine monophosphate (AMP) explains. Cycling of the 'A' moiety accelerates when the cell's energy state is endangered, another essential domino among the seven required for understanding of the experimental observations. This new domino analysis shows how strategic experimental design and observations in tandem with theory and modeling may identify and resolve important paradoxes. It also highlights the hitherto unexpected role of the 'A' component of ATP.
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Affiliation(s)
- Malkhey Verma
- Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
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22
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Regulation of amino acid, nucleotide, and phosphate metabolism in Saccharomyces cerevisiae. Genetics 2012; 190:885-929. [PMID: 22419079 DOI: 10.1534/genetics.111.133306] [Citation(s) in RCA: 348] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ever since the beginning of biochemical analysis, yeast has been a pioneering model for studying the regulation of eukaryotic metabolism. During the last three decades, the combination of powerful yeast genetics and genome-wide approaches has led to a more integrated view of metabolic regulation. Multiple layers of regulation, from suprapathway control to individual gene responses, have been discovered. Constitutive and dedicated systems that are critical in sensing of the intra- and extracellular environment have been identified, and there is a growing awareness of their involvement in the highly regulated intracellular compartmentalization of proteins and metabolites. This review focuses on recent developments in the field of amino acid, nucleotide, and phosphate metabolism and provides illustrative examples of how yeast cells combine a variety of mechanisms to achieve coordinated regulation of multiple metabolic pathways. Importantly, common schemes have emerged, which reveal mechanisms conserved among various pathways, such as those involved in metabolite sensing and transcriptional regulation by noncoding RNAs or by metabolic intermediates. Thanks to the remarkable sophistication offered by the yeast experimental system, a picture of the intimate connections between the metabolomic and the transcriptome is becoming clear.
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23
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5-Aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-Monophosphate (AICAR), a Highly Conserved Purine Intermediate with Multiple Effects. Metabolites 2012; 2:292-302. [PMID: 24957512 PMCID: PMC3901205 DOI: 10.3390/metabo2020292] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 03/15/2012] [Accepted: 03/16/2012] [Indexed: 12/25/2022] Open
Abstract
AICAR (5-Aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate) is a natural metabolic intermediate of purine biosynthesis that is present in all organisms. In yeast, AICAR plays important regulatory roles under physiological conditions, notably through its direct interactions with transcription factors. In humans, AICAR accumulates in several metabolic diseases, but its contribution to the symptoms has not yet been elucidated. Further, AICAR has highly promising properties which have been recently revealed. Indeed, it enhances endurance of sedentary mice. In addition, it has antiproliferative effects notably by specifically inducing apoptosis of aneuploid cells. Some of the effects of AICAR are due to its ability to stimulate the AMP-activated protein kinase but some others are not. It is consequently clear that AICAR affects multiple targets although only few of them have been identified so far. This review proposes an overview of the field and suggests future directions.
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24
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Servant G, Pinson B, Tchalikian-Cosson A, Coulpier F, Lemoine S, Pennetier C, Bridier-Nahmias A, Todeschini AL, Fayol H, Daignan-Fornier B, Lesage P. Tye7 regulates yeast Ty1 retrotransposon sense and antisense transcription in response to adenylic nucleotides stress. Nucleic Acids Res 2012; 40:5271-82. [PMID: 22379133 PMCID: PMC3384299 DOI: 10.1093/nar/gks166] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Transposable elements play a fundamental role in genome evolution. It is proposed that their mobility, activated under stress, induces mutations that could confer advantages to the host organism. Transcription of the Ty1 LTR-retrotransposon of Saccharomyces cerevisiae is activated in response to a severe deficiency in adenylic nucleotides. Here, we show that Ty2 and Ty3 are also stimulated under these stress conditions, revealing the simultaneous activation of three active Ty retrotransposon families. We demonstrate that Ty1 activation in response to adenylic nucleotide depletion requires the DNA-binding transcription factor Tye7. Ty1 is transcribed in both sense and antisense directions. We identify three Tye7 potential binding sites in the region of Ty1 DNA sequence where antisense transcription starts. We show that Tye7 binds to Ty1 DNA and regulates Ty1 antisense transcription. Altogether, our data suggest that, in response to adenylic nucleotide reduction, TYE7 is induced and activates Ty1 mRNA transcription, possibly by controlling Ty1 antisense transcription. We also provide the first evidence that Ty1 antisense transcription can be regulated by environmental stress conditions, pointing to a new level of control of Ty1 activity by stress, as Ty1 antisense RNAs play an important role in regulating Ty1 mobility at both the transcriptional and post-transcriptional stages.
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Affiliation(s)
- Géraldine Servant
- CNRS UPR9073, associated with Univ Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-chimique, F-75005 Paris, France
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25
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Hürlimann HC, Laloo B, Simon-Kayser B, Saint-Marc C, Coulpier F, Lemoine S, Daignan-Fornier B, Pinson B. Physiological and toxic effects of purine intermediate 5-amino-4-imidazolecarboxamide ribonucleotide (AICAR) in yeast. J Biol Chem 2011; 286:30994-31002. [PMID: 21757731 DOI: 10.1074/jbc.m111.262659] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
5-Amino-4-imidazolecarboxamide ribonucleotide 5'-phosphate (AICAR) is a monophosphate metabolic intermediate of the de novo purine synthesis pathway that has highly promising metabolic and antiproliferative properties. Yeast mutants unable to metabolize AICAR are auxotroph for histidine. A screening for suppressors of this phenotype identified recessive and dominant mutants that result in lowering the intracellular AICAR concentration. The recessive mutants affect the adenosine kinase, which is shown here to catalyze the phosphorylation of AICAR riboside in yeast. The dominant mutants strongly enhance the capacity of the alkaline phosphatase Pho13 to dephosphorylate 5-amino-4-imidazole N-succinocarboxamide ribonucleotide 5'-phosphate(SAICAR) into its non-toxic riboside form. By combining these mutants with transcriptomics and metabolomics analyses, we establish that in yeast responses to AICAR and SAICAR are clearly linked to the concentration of the monophosphate forms, whereas the derived nucleoside moieties have no effect even at high intracellular concentration. Finally, we show that AICAR/SAICAR concentrations vary under physiological conditions known to modulate transcription of the purine and phosphate pathway genes.
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Affiliation(s)
- Hans C Hürlimann
- Institut de Biochimie et Génétique Cellulaires (IBGC) Unité Mixte de Recherche (UMR) 5095, Université Ségalen, Bordeaux F-33077, France; IBGC UMR 5095, CNRS, Bordeaux F-33077, France
| | - Benoît Laloo
- Institut de Biochimie et Génétique Cellulaires (IBGC) Unité Mixte de Recherche (UMR) 5095, Université Ségalen, Bordeaux F-33077, France; IBGC UMR 5095, CNRS, Bordeaux F-33077, France
| | - Barbara Simon-Kayser
- Institut de Biochimie et Génétique Cellulaires (IBGC) Unité Mixte de Recherche (UMR) 5095, Université Ségalen, Bordeaux F-33077, France; IBGC UMR 5095, CNRS, Bordeaux F-33077, France
| | - Christelle Saint-Marc
- Institut de Biochimie et Génétique Cellulaires (IBGC) Unité Mixte de Recherche (UMR) 5095, Université Ségalen, Bordeaux F-33077, France; IBGC UMR 5095, CNRS, Bordeaux F-33077, France
| | - Fanny Coulpier
- Institut de Biologie de l'ENS, IBENS, École normale supérieure (ENS), Paris F-75005, France; INSERM, U1024, Paris F-75005, France; UMR 8197, CNRS, Paris F-75005, France
| | - Sophie Lemoine
- Institut de Biologie de l'ENS, IBENS, École normale supérieure (ENS), Paris F-75005, France; INSERM, U1024, Paris F-75005, France; UMR 8197, CNRS, Paris F-75005, France
| | - Bertrand Daignan-Fornier
- Institut de Biochimie et Génétique Cellulaires (IBGC) Unité Mixte de Recherche (UMR) 5095, Université Ségalen, Bordeaux F-33077, France; IBGC UMR 5095, CNRS, Bordeaux F-33077, France.
| | - Benoît Pinson
- Institut de Biochimie et Génétique Cellulaires (IBGC) Unité Mixte de Recherche (UMR) 5095, Université Ségalen, Bordeaux F-33077, France; IBGC UMR 5095, CNRS, Bordeaux F-33077, France
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26
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Sambuk EV, Fizikova AY, Savinov VA, Padkina MV. Acid phosphatases of budding yeast as a model of choice for transcription regulation research. Enzyme Res 2011; 2011:356093. [PMID: 21785706 PMCID: PMC3137970 DOI: 10.4061/2011/356093] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 04/26/2011] [Indexed: 11/20/2022] Open
Abstract
Acid phosphatases of budding yeast have been studied for more than forty years. This paper covers biochemical characteristics of acid phosphatases and different aspects in expression regulation of eukaryotic genes, which were researched using acid phosphatases model. A special focus is devoted to cyclin-dependent kinase Pho85p, a negative transcriptional regulator, and its role in maintaining mitochondrial genome stability and to pleiotropic effects of pho85 mutations.
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Affiliation(s)
- Elena V Sambuk
- Genetics and Breeding Department, Biology and Soil Sciences Faculty, Saint Petersburg State University, Universitetskaya emb. 7-9, Saint Petersburg 199034, Russia
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27
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Lu SP, Lin SJ. Phosphate-responsive signaling pathway is a novel component of NAD+ metabolism in Saccharomyces cerevisiae. J Biol Chem 2011; 286:14271-81. [PMID: 21349851 DOI: 10.1074/jbc.m110.217885] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD(+)) is an essential cofactor involved in various cellular biochemical reactions. To date the signaling pathways that regulate NAD(+) metabolism remain unclear due to the dynamic nature and complexity of the NAD(+) metabolic pathways and the difficulty of determining the levels of the interconvertible pyridine nucleotides. Nicotinamide riboside (NmR) is a key pyridine metabolite that is excreted and re-assimilated by yeast and plays important roles in the maintenance of NAD(+) pool. In this study we establish a NmR-specific reporter system and use it to identify yeast mutants with altered NmR/NAD(+) metabolism. We show that the phosphate-responsive signaling (PHO) pathway contributes to control NAD(+) metabolism. Yeast strains with activated PHO pathway show increases in both the release rate and internal concentration of NmR. We further identify Pho8, a PHO-regulated vacuolar phosphatase, as a potential NmR production factor. We also demonstrate that Fun26, a homolog of human ENT (equilibrative nucleoside transporter), localizes to the vacuolar membrane and establishes the size of the vacuolar and cytosolic NmR pools. In addition, the PHO pathway responds to depletion of cellular nicotinic acid mononucleotide (NaMN) and mediates nicotinamide mononucleotide (NMN) catabolism, thereby contributing to both NmR salvage and phosphate acquisition. Therefore, NaMN is a putative molecular link connecting the PHO signaling and NAD(+) metabolic pathways. Our findings may contribute to the understanding of the molecular basis and regulation of NAD(+) metabolism in higher eukaryotes.
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Affiliation(s)
- Shu-Ping Lu
- Department of Microbiology, College of Biological Sciences, University of California, Davis, California 95616, USA
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28
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Couthouis J, Marchal C, D'Angelo F, Berthelot K, Cullin C. The toxicity of an "artificial" amyloid is related to how it interacts with membranes. Prion 2010; 4:283-91. [PMID: 21057225 DOI: 10.4161/pri.4.4.13126] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Despite intensive research into how amyloid structures can impair cellular viability, the molecular nature of these toxic species and the cellular mechanisms involved are not clearly defined and may differ from one disease to another. We systematically analyzed, in Saccharomyces cerevisiae, genes that increase the toxicity of an amyloid (M8), previously selected in yeast on the sole basis of its cellular toxicity (and consequently qualified as "artificial"). This genomic screening identified the Vps-C HOPS (homotypic vacuole fusion and protein sorting) complex as a key-player in amyloid toxicity. This finding led us to analyze further the phenotype induced by M8 expression. M8-expressing cells displayed an identical phenotype to vps mutants in terms of endocytosis, vacuolar morphology and salt sensitivity. The direct and specific interaction between M8 and lipids reinforces the role of membrane formation in toxicity due to M8. Together these findings suggest a model in which amyloid toxicity results from membrane fission.
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Affiliation(s)
- Julien Couthouis
- IBGC, UMR 5095, CNRS, Université Bordeaux 2 Victor Segalen, Bordeaux, France
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29
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Cheng X, Xu Z, Wang J, Zhai Y, Lu Y, Liang C. ATP-dependent pre-replicative complex assembly is facilitated by Adk1p in budding yeast. J Biol Chem 2010; 285:29974-80. [PMID: 20659900 PMCID: PMC2943264 DOI: 10.1074/jbc.m110.161455] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 07/16/2010] [Indexed: 01/30/2023] Open
Abstract
Pre-replicative complex (pre-RC) assembly is a critical part of the mechanism that controls the initiation of DNA replication, and ATP binding and hydrolysis by multiple pre-RC proteins are essential for pre-RC assembly and activation. Here, we demonstrate that Adk1p (adenylate kinase 1 protein) plays an important role in pre-RC assembly in Saccharomyces cerevisiae. Isolated from a genetic screen, adk1(G20S) cells with a mutation within the nucleotide-binding site were defective in replication initiation. adk1Δ cells were viable at 25 °C but not at 37°C. Flow cytometry indicated that both the adk1-td (temperature-inducible degron) and adk1(G20S) mutants were defective in S phase entry. Furthermore, Adk1p bound to chromatin throughout the cell cycle and physically interacted with Orc3p, whereas the Adk1(G20S) protein had a reduced ability to bind chromatin and Orc3p without affecting the cellular ATP level. In addition, Adk1p associated with replication origins by ChIP assay. Finally, Adk1-td protein depletion prevented pre-RC assembly during the M-to-G(1) transition. We suggest that Adk1p regulates ATP metabolism on pre-RC proteins to promote pre-RC assembly and activation.
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Affiliation(s)
- Xue Cheng
- From the Section of Biochemistry and Cell Biology, Division of Life Science, and the Center for Cancer Research, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and
| | - Zhen Xu
- From the Section of Biochemistry and Cell Biology, Division of Life Science, and the Center for Cancer Research, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and
| | - Jiafeng Wang
- From the Section of Biochemistry and Cell Biology, Division of Life Science, and the Center for Cancer Research, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and
- the School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanliang Zhai
- From the Section of Biochemistry and Cell Biology, Division of Life Science, and the Center for Cancer Research, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and
| | - Yongjun Lu
- the School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chun Liang
- From the Section of Biochemistry and Cell Biology, Division of Life Science, and the Center for Cancer Research, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China and
- the School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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30
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Matecic M, Smith DL, Pan X, Maqani N, Bekiranov S, Boeke JD, Smith JS. A microarray-based genetic screen for yeast chronological aging factors. PLoS Genet 2010; 6:e1000921. [PMID: 20421943 PMCID: PMC2858703 DOI: 10.1371/journal.pgen.1000921] [Citation(s) in RCA: 163] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 03/24/2010] [Indexed: 11/18/2022] Open
Abstract
Model organisms have played an important role in the elucidation of multiple genes and cellular processes that regulate aging. In this study we utilized the budding yeast, Saccharomyces cerevisiae, in a large-scale screen for genes that function in the regulation of chronological lifespan, which is defined by the number of days that non-dividing cells remain viable. A pooled collection of viable haploid gene deletion mutants, each tagged with unique identifying DNA “bar-code” sequences was chronologically aged in liquid culture. Viable mutants in the aging population were selected at several time points and then detected using a microarray DNA hybridization technique that quantifies abundance of the barcode tags. Multiple short- and long-lived mutants were identified using this approach. Among the confirmed short-lived mutants were those defective for autophagy, indicating a key requirement for the recycling of cellular organelles in longevity. Defects in autophagy also prevented lifespan extension induced by limitation of amino acids in the growth media. Among the confirmed long-lived mutants were those defective in the highly conserved de novo purine biosynthesis pathway (the ADE genes), which ultimately produces IMP and AMP. Blocking this pathway extended lifespan to the same degree as calorie (glucose) restriction. A recently discovered cell-extrinsic mechanism of chronological aging involving acetic acid secretion and toxicity was suppressed in a long-lived ade4Δ mutant and exacerbated by a short-lived atg16Δ autophagy mutant. The identification of multiple novel effectors of yeast chronological lifespan will greatly aid in the elucidation of mechanisms that cells and organisms utilize in slowing down the aging process. The aging process is associated with the onset of several age-associated diseases including diabetes and cancer. In rodent model systems, the dietary regimen known as caloric restriction (CR) is known to delay or prevent these diseases and to extend lifespan. As a result, there is a great deal of interest in understanding the mechanisms by which CR functions. The budding yeast, Saccharomyces cerevisiae, has proven to be an effective model for the analysis of genes and cellular pathways that contribute to the regulation of aging. In this study we have performed a microarray-based genetic screen in yeast that identified short- and long-lived mutants from a population that contained each of the viable haploid gene deletion mutants from the yeast gene knockout collection that were pooled together. Using such an approach, we were able to identify genes from several pathways that had not been previously implicated in aging, including some that appear to contribute to the CR effect induced by restriction of either amino acids or sugar. These results are expected to provide new groundwork for future mechanistic aging studies in more complex organisms.
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Affiliation(s)
- Mirela Matecic
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, School of Medicine, Charlottesville, Virginia, United States of America
| | - Daniel L. Smith
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, School of Medicine, Charlottesville, Virginia, United States of America
| | - Xuewen Pan
- Department of Molecular Biology and Genetics, High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Nazif Maqani
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, School of Medicine, Charlottesville, Virginia, United States of America
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, School of Medicine, Charlottesville, Virginia, United States of America
| | - Jef D. Boeke
- Department of Molecular Biology and Genetics, High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jeffrey S. Smith
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, School of Medicine, Charlottesville, Virginia, United States of America
- * E-mail:
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Life in the midst of scarcity: adaptations to nutrient availability in Saccharomyces cerevisiae. Curr Genet 2010; 56:1-32. [PMID: 20054690 DOI: 10.1007/s00294-009-0287-1] [Citation(s) in RCA: 163] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 12/18/2009] [Accepted: 12/19/2009] [Indexed: 12/27/2022]
Abstract
Cells of all living organisms contain complex signal transduction networks to ensure that a wide range of physiological properties are properly adapted to the environmental conditions. The fundamental concepts and individual building blocks of these signalling networks are generally well-conserved from yeast to man; yet, the central role that growth factors and hormones play in the regulation of signalling cascades in higher eukaryotes is executed by nutrients in yeast. Several nutrient-controlled pathways, which regulate cell growth and proliferation, metabolism and stress resistance, have been defined in yeast. These pathways are integrated into a signalling network, which ensures that yeast cells enter a quiescent, resting phase (G0) to survive periods of nutrient scarceness and that they rapidly resume growth and cell proliferation when nutrient conditions become favourable again. A series of well-conserved nutrient-sensory protein kinases perform key roles in this signalling network: i.e. Snf1, PKA, Tor1 and Tor2, Sch9 and Pho85-Pho80. In this review, we provide a comprehensive overview on the current understanding of the signalling processes mediated via these kinases with a particular focus on how these individual pathways converge to signalling networks that ultimately ensure the dynamic translation of extracellular nutrient signals into appropriate physiological responses.
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32
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Fission yeast Iec1-ino80-mediated nucleosome eviction regulates nucleotide and phosphate metabolism. Mol Cell Biol 2009; 30:657-74. [PMID: 19933844 DOI: 10.1128/mcb.01117-09] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Ino80 is an ATP-dependent nucleosome-remodeling enzyme involved in transcription, replication, and the DNA damage response. Here, we characterize the fission yeast Ino80 and find that it is essential for cell viability. We show that the Ino80 complex from fission yeast mediates ATP-dependent nucleosome remodeling in vitro. The purification of the Ino80-associated complex identified a highly conserved complex and the presence of a novel zinc finger protein with similarities to the mammalian transcriptional regulator Yin Yang 1 (YY1) and other members of the GLI-Krüppel family of proteins. Deletion of this Iec1 protein or the Ino80 complex subunit arp8, ies6, or ies2 causes defects in DNA damage repair, the response to replication stress, and nucleotide metabolism. We show that Iec1 is important for the correct expression of genes involved in nucleotide metabolism, including the ribonucleotide reductase subunit cdc22 and phosphate- and adenine-responsive genes. We find that Ino80 is recruited to a large number of promoter regions on phosphate starvation, including those of phosphate- and adenine-responsive genes that depend on Iec1 for correct expression. Iec1 is required for the binding of Ino80 to target genes and subsequent histone loss at the promoter and throughout the body of these genes on phosphate starvation. This suggests that the Iec1-Ino80 complex promotes transcription through nucleosome eviction.
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33
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Phenotypic consequences of purine nucleotide imbalance in Saccharomyces cerevisiae. Genetics 2009; 183:529-38, 1SI-7SI. [PMID: 19635936 DOI: 10.1534/genetics.109.105858] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Coordinating homeostasis of multiple metabolites is a major task for living organisms, and complex interconversion pathways contribute to achieving the proper balance of metabolites. AMP deaminase (AMPD) is such an interconversion enzyme that allows IMP synthesis from AMP. In this article, we show that, under specific conditions, lack of AMPD activity impairs growth. Under these conditions, we found that the intracellular guanylic nucleotide pool was severely affected. In vivo studies of two AMPD homologs, Yjl070p and Ybr284p, indicate that these proteins have no detectable AMP, adenosine, or adenine deaminase activity; we show that overexpression of YJL070c instead mimics a loss of AMPD function. Expression of the yeast transcriptome was monitored in a AMPD-deficient mutant in a strain overexpressing YJL070c and in cells treated with the immunosuppressive drug mycophenolic acid, three conditions that lead to severe depletion of the guanylic nucleotide pool. These three conditions resulted in the up- or downregulation of multiple transcripts, 244 of which are common to at least two conditions and 71 to all three conditions. These transcriptome results, combined with specific mutant analysis, point to threonine metabolism as exquisitely sensitive to the purine nucleotide balance.
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34
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Pinson B, Vaur S, Sagot I, Coulpier F, Lemoine S, Daignan-Fornier B. Metabolic intermediates selectively stimulate transcription factor interaction and modulate phosphate and purine pathways. Genes Dev 2009; 23:1399-407. [PMID: 19528318 PMCID: PMC2701576 DOI: 10.1101/gad.521809] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 04/29/2009] [Indexed: 01/04/2023]
Abstract
Cells use strategic metabolites to sense the metabolome and accordingly modulate gene expression. Here, we show that the purine and phosphate pathways are positively regulated by the metabolic intermediate AICAR (5'-phosphoribosyl-5-amino-4-imidazole carboxamide). The transcription factor Pho2p is required for up-regulation of all AICAR-responsive genes. Accordingly, the binding of Pho2p to purine and phosphate pathway gene promoters is enhanced upon AICAR accumulation. In vitro, AICAR binds both Pho2p and Pho4p transcription factors and stimulates the interaction between Pho2p and either Bas1p or Pho4p in vivo. In contrast, SAICAR (succinyl-AICAR) only affects Pho2p-Bas1p interaction and specifically up-regulates purine regulon genes. Together, our data show that Bas1p and Pho4p compete for Pho2p binding, hence leading to the concerted regulation of cellular nucleotide synthesis and phosphate consumption.
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Affiliation(s)
- Benoît Pinson
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, Bordeaux 33076, France
- CNRS, UMR5095, Bordeaux, 33077 Cedex, France
| | - Sabine Vaur
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, Bordeaux 33076, France
- CNRS, UMR5095, Bordeaux, 33077 Cedex, France
| | - Isabelle Sagot
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, Bordeaux 33076, France
- CNRS, UMR5095, Bordeaux, 33077 Cedex, France
| | - Fanny Coulpier
- IFR36, Plate-forme Transcriptome, École Normale Supérieure, Paris 75230, France
| | - Sophie Lemoine
- IFR36, Plate-forme Transcriptome, École Normale Supérieure, Paris 75230, France
| | - Bertrand Daignan-Fornier
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, Bordeaux 33076, France
- CNRS, UMR5095, Bordeaux, 33077 Cedex, France
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35
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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